AMBER Archive (2009)

Subject: Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file

From: Crowley, Michael (Michael.Crowley_at_nrel.gov)
Date: Sat Oct 31 2009 - 12:32:12 CDT

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----- Original Message -----
From: amber-bounces_at_ambermd.org <amber-bounces_at_ambermd.org>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Sat Oct 31 09:10:12 2009
Subject: Re: [AMBER] Lennard Jones Potential A and B coefficients in Topology file

On Sat, 31 Oct 2009 10:59:14 -0400, Tom Joseph <ttjoseph_at_gmail.com> wrote:
> 2009/10/31 Tom Joseph <ttjoseph_at_gmail.com>:
>> According to the documentation it's not NTYPES x NTYPES, it is
>> NTYPES*(NTYPES+1)/2), which you can verify by looking at a valid
>> prmtop file.
>
> To be clear, I was referring to the LENNARD_JONES_ACOEF,
> LENNARD_JONES_BCOEF, etc blocks. The NONBONDED_PARM_INDEX, which
> indexes these arrays, is indeed NTYPES x NTYPES in length.

Yep, I have seen this, thanks for all your answers Tom. I will try to see
clearer and check if I can get accurately the information I want (just an
indexing game if I understand well)...but for now I have to solve some
hardware problems first ;)

Peter

> --Tom
>
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